Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles

Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles

Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.

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Main Authors: Fay, Jessica Vannina, Watkins, Christopher J., Shrestha, Ram K., Litwiñiuk, Sergio Leandro, Talavera Stefani, Liliana Noelia, Rojas, Cristian A., Argüelles, Carina Francisca, Ferreras, Julián Alberto, Cáccamo, Mario José, Miretti, Marcos Mateo
Format: info:eu-repo/semantics/article biblioteca
Language:eng
Published: BioMed Central
Subjects:Ilex paraguariensis, Yerba mate, Transcriptome, Expression profile, Functional annotation, De-novo assembly, Phenylpropanoid,
Online Access:https://hdl.handle.net/20.500.12219/4325
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id dig-ridunam-ar-20.500.12219-4325
record_format koha
institution UNAM AR
collection DSpace
country Argentina
countrycode AR
component Bibliográfico
access En linea
databasecode dig-ridunam-ar
tag biblioteca
region America del Sur
libraryname Biblioteca Regional ElDorado
language eng
topic Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
spellingShingle Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
Fay, Jessica Vannina
Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
description Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina.
format info:eu-repo/semantics/article
topic_facet Ilex paraguariensis
Yerba mate
Transcriptome
Expression profile
Functional annotation
De-novo assembly
Phenylpropanoid
author Fay, Jessica Vannina
Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
author_facet Fay, Jessica Vannina
Watkins, Christopher J.
Shrestha, Ram K.
Litwiñiuk, Sergio Leandro
Talavera Stefani, Liliana Noelia
Rojas, Cristian A.
Argüelles, Carina Francisca
Ferreras, Julián Alberto
Cáccamo, Mario José
Miretti, Marcos Mateo
author_sort Fay, Jessica Vannina
title Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_short Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_full Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_fullStr Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_full_unstemmed Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
title_sort yerba mate (ilex paraguariensis, a. st.-hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles
publisher BioMed Central
url https://hdl.handle.net/20.500.12219/4325
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spelling dig-ridunam-ar-20.500.12219-43252024-06-03T12:56:38Z Yerba mate (Ilex paraguariensis, A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles Fay, Jessica Vannina Watkins, Christopher J. Shrestha, Ram K. Litwiñiuk, Sergio Leandro Talavera Stefani, Liliana Noelia Rojas, Cristian A. Argüelles, Carina Francisca Ferreras, Julián Alberto Cáccamo, Mario José Miretti, Marcos Mateo Ilex paraguariensis Yerba mate Transcriptome Expression profile Functional annotation De-novo assembly Phenylpropanoid Fil: Fay, Jessica Vannina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Fay, Jessica Vannina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina. Fil: Watkins, Christopher J. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido. Fil: Watkins, Christopher J. Norwich Research Park. Earlham Institute; Reino Unido. Fil: Shrestha, Ram K. Norwich Research Park. Centro de Análisis del Genoma; Reino Unido. Fil: Shrestha, Ram K. Norwich Research Park. Earlham Institute; Reino Unido. Fil: Litwiñiuk, Sergio Leandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Litwiñiuk, Sergio Leandro. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina. Fil: Talavera Stefani, Liliana Noelia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Talavera Stefani, Liliana Noelia. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina. Fil: Rojas, Cristian A. Universidad Federal de la Integración Latinoamericana; Brasil. Fil: Argüelles, Carina Francisca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Argüelles, Carina Francisca. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina. Fil: Ferreras, Julian Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Ferreras, Julian Alberto. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Instituto de Biología Subtropical; Argentina. Fil: Cáccamo, Mario José. Parque de investigación de Norwich. Centro de Análisis del Genoma; Reino Unido. Fil: Cáccamo, Mario José. Instituto Nacional de Botánica Agropecuaria. Parque de investigación de Norwich; Reino Unido. Fil: Miretti, Marcos Mateo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico (Nordeste). Instituto de Biología Subtropical; Argentina. Fil: Miretti, Marcos Mateo. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Química y Naturales. Instituto de Biología Subtropical; Argentina. Background: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. Results: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. Conclusions: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves’ polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites. 2018-12-07 info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion https://hdl.handle.net/20.500.12219/4325 eng info:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5240-6 info:eu-repo/semantics/openAccess application/pdf application/pdf 2.639 MB BioMed Central

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